Small molecules identified in previous HTS increase GCase activity.

The lower extent of these error bars is not visible. Avoid “dynamite plots”

We can’t see difference between effects of two concentrations of A16 in (D), or A16 vs A18 in (B); use a table of contrasts. [Leighton to maybe edit this; figure needs editing]

Place things to be compared by the reader next to each other where possible.

The scale on the micrographs (especially in panel C) is too small to read easily.

In addition to showing DAPI and immunofluorescence images of the cells, we should really be seeing a bright-field micrograph of the cells (no fluorescence).

The colour scheme is misleading (compare 1 \(\mu\)M A18 in B vs 5 \(\mu\)M in D)

Too many comparisons in B - avoid cluttering figures with “chartjunk”

y-axes should really have the same scale in all plots, to make intra-panel comparisons easier

Endometriosis-associated macrophages exhibit significant transcriptomic heterogeneity.

UMAP plots (B, E) are highly manipulable and clustering/placement does not necessarily reflect objective measures.

Unpleasant colour choices in (C); there is room for aesthetic improvement

The proportion plot in (C) does not give information on absolute number, only proportion; a proportional areas plot spanning all clusters would more honestly represent the data

Heatmap text is too small to read comfortably; is there too much data here?

Heatmap is missing a scale (is purple high and yellow low, or vice versa?)

The flow diagram (A) could make better use of arrows to illustrate order of steps

Text overall is too small, and hard to read comfortably

Whitespace usage could be improved, and the overall flow of the figure - in particular, cramming (C) under the inset from (B) makes the figure feel very crowded

Consider what is needed to convey the figure’s intended message: if it’s just that these macrophages exhibit transcriptional heterogeneity, then D is probably sufficient for that purpose; if it is some other message, then revise for clarity.

A C. difficile mutant lacking all three YkuD-type Ldts (Δldt1-3) exhibits wild-type growth, morphology, and 3-3 cross-linking.

The lower extent of error bars is not visible in (D) or (E). These are “dynamite plots,” which should be avoided

Bar charts should be avoided in general; a 1D scatterplot of each dataset in (D) and (E) would be clearer

Failure to complement the triple mutant strain - missing data??? This is a control I would expect to see for these experiments.

Labels should not be placed where they obscure part of an image.

Fluorescence wavelength not specified

Colour scheme in (A), and between B and D/E, is inconsistent - more rational, and helpful, colour choices could be made here.

Axis label in (B) could be improved - OD₆₀₀ is not very informative.

Figure legend for (A) could be more succinct/some of this info should be in the paper text instead. Overall a figure legend should provide enough detail for the figure to stand alone, but should not describe results/significance.

Functional characterization and overall structure of Rv1217c–1218c.

The rifampicin structure is purely decorative and could be removed - avoid needless distractions in figures.

The lower extent of error bars is not visible in (B). This is a “dynamite plot,” which should be avoided

Bar charts should be avoided in general; a 1D scatterplot of each dataset in (B) would be clearer.

Colour scheme in (B) doesn’t seem purposeful and doesn’t add anything to the figure

The implied membrane in (C) and (D) could be stated as such in the figure.

By convention in microbiology, we would assume that the periplasm/extracellular space is “up” and the cytoplasm is “down” in (C) and (D) - but this should really be labelled to avoid any potential confusion.

Colours in (A) difficult to distinguish, especially with the red boxes which seem to skew blue closer to purple - this could be presented more clearly.

Showing two cut-out bands is not an appropriate way to show Western blot data - show the whole blot

Text in (D) is too small to read easily